GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Flandrois Jean-Pierre

Professeur d'université émérite

UCBL

Address: 43 Bd du 11 novembre 1918
69622 VILLEURBANNE

Tel: 04 72 44 85 60

Email

Linkedin

My Research

Two flagship projects

BIBI-DB BIBI-DB is a taxonomy-hierarchized set of databases and oriented to facilitate the phylogeny of Archaea and Bacteria. Thanks to a web interface it allows the phylogenetic placement of unknown nucleic acid sequences (this may precede identification). RiboDB is a ribosomal protein database of Bacteria and Archaea freely searchable via the Internet. RiboDB construction process is versatile and can be used to construct proteins databases from freshly assembled and annotated genomes.

Applications

leBIBI is a web application used worldwide to identify bacteria in hospital laboratories, industrial, environmental.
The leBIBI and RiboDB databases are useful to classify more rigorously the Bacteria and Archaea and may highlight new pathogen species. Their use helps to explain the evolution of the microbial world. RiboDB will allow to improve the quality of diagnosis of infections. 

Ancient Ecosystems and stable isotopes

I am very pleased to cooperate since 2012 in some work Christophe Lecuyer and his team as a physiologist, biologist and physician. This topic is now a real scientific center of interest for me!

The first studies were on ancient climates reconstruction by using the informations recorded in bone and teeth of egyptian mummies but of course we get also informations on human and animal nutrition. 
Climate reconstruction may also be done outside egypt with other types of samples.

We were also proud to show that the hatching temperature of Oviraptosaurs were not so different from that of actual birds... 

 

Medical microbiology

This are works I have initiated or using datas that have been collected during my previous position as Head of the Microbiology Laboratory CH Lyon-Sud 1979-2013.

Publications

Display of 31 to 60 publications on 137 in total

Oxygen isotope fractionation between bird eggshell calcite and body water: application to fossil eggs from Lanzarote (Canary Islands)

Nicolas Lazzerini, Christophe Lécuyer, Romain Amiot, Delphine Angst, Eric Buffetaut, François Fourel...

The Science of Nature Naturwissenschaften . 103 ( 9-10 )

DOI: 10.1007/s00114-016-1404-x

Journal article

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RiboDB database: a comprehensive resource for prokaryotic systematics

Frédéric Jauffrit, Simon Penel, Stéphane Delmotte, Carine Rey, Damien M de Vienne, Manolo Gouy...

Molecular Biology and Evolution . 33 ( 8 ) : 2170--2172

DOI: 10.1093/molbev/msw088

Journal article

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Combined Genotypic, Phylogenetic, and Epidemiologic Analyses of Mycobacterium tuberculosis Genetic Diversity in the Rhône Alpes Region, France

Catherine Pichat, David Couvin, Gérard Carret, Isabelle Frédénucci, Véronique Jacomo, Anne Carricajo...

PLoS ONE . 11 ( 4 ) : e0153580

DOI: 10.1371/journal.pone.0153580

Journal article

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Assessment of polycarbonate filter in a molecular analytical system for the microbiological quality monitoring of recycled waters onboard ISS

Anne-Laure Bechy-Loizeau, Jean-Pierre Flandrois, Hafid Abaibou

Life Sciences in Space Research . 6 : 29-35

DOI: 10.1016/j.lssr.2015.06.002

Journal article

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Nontuberculous Mycobacteria: An Underestimated Cause of Bioprosthetic Valve Infective Endocarditis

C. Bouchiat, J. Saison, S. Boisset, Jean-Pierre Flandrois, B. Issartel, O. Dauwalder...

Open Forum Infectious Diseases . 2 ( 2 )

DOI: 10.1093/ofid/ofv047

Journal article

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leBIBIQBPP: a set of databases and a webtool for automatic phylogenetic analysis of prokaryotic sequences

Jean-Pierre Flandrois, G. Perrière, Manolo Gouy

BMC Bioinformatics . 16 ( 1 ) : 251

DOI: 10.1186/s12859-015-0692-z

Journal article

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A Toolbox for Nonlinear Regression in R: The Package nistools

F. Baty, C. Ritz, Sandrine Charles, M. Brutsche, Jean-Pierre Flandrois, Marie Laure Delignette-Muller

Journal of Statistical Software . 66 : 1-21

Journal article

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Diet of ancient Egyptians inferred from stable isotope systematics

Alexandra Touzeau, Romain Amiot, Janne Blichert-Toft, Jean-Pierre Flandrois, François Fourel, Vincent Grossi...

Journal of Archaeological Science . 46 : 114-124

DOI: 10.1016/j.jas.2014.03.005

Journal article

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MUBII-TB-DB: a database of mutations associated with antibiotic resistance in Mycobacterium tuberculosis.

Jean-Pierre Flandrois, Gérard Lina, Oana Dumitrescu

BMC Bioinformatics . 15 ( 1 ) : 107

DOI: 10.1186/1471-2105-15-107

Journal article

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Mycobacterium Species Related to M. leprae and M. lepromatosis from Cows with Bovine Nodular Thelitis

D. Pin, V. Guerin-Faublee, V. Garreau, F. Breysse, Oana Dumitrescu, Jean-Pierre Flandrois...

Emerging Infectious Diseases . 20 : 2111-4

DOI: 10.3201/eid2012.140184

Journal article

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Optimization of the reactional medium and a food impact study for a colorimetric in situ Salmonella spp. detection method

L. Morand, D. Michel, Jean-Pierre Flandrois, T. Junillon, D. Mosticon, B. Mallen...

International Journal of Food Microbiology . 181 : 48-52

Journal article

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Enhanced tetrazolium violet reduction of Salmonella spp. by magnesium addition to the culture media

T. Junillon, L. Morand, Jean-Pierre Flandrois

Food Microbiology . 42 : 132-135

Journal article

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Diminution of 2,3,5-triphenyltetrazolium chloride toxicity on Listeria monocytogenes growth by iron source addition to the culture medium

T. Junillon, Jp. Flandrois

Food Microbiology . 38 : 1--5

DOI: 10.1016/j.fm.2013.07.005

Journal article

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Mycobacterium bourgelatii sp. nov., a rapidly growing, non-chromogenic species isolated from the lymph nodes of cattle.

Véronique Guérin-Faublée, Jean-Pierre Flandrois, Catherine Pichat, Maria Laura Boschiroli, Brigitte Lamy

International Journal of Systematic and Evolutionary Microbiology . 63 ( Pt 12 ) : 4669-74

DOI: 10.1099/ijs.0.051979-0

Journal article

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Candida albicans and non- Candida albicans fungemia in an institutional hospital during a decade

Jean-Pierre Flandrois, Laurence Parmeland, Mathieu Gazon, Claude Guérin, Laurent Argaud, Jean-Jacques Lehot...

Medical Mycology . 51 ( 1 ) : 33-37

DOI: 10.3109/13693786.2012.686673

Journal article

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Egyptian mummies record increasing aridity in the Nile valley from 5500 to 1500yr before present

Alexandra Touzeau, Janne Blichert-Toft, Romain Amiot, François Fourel, François Martineau, Jenefer Cockitt...

Earth and Planetary Science Letters . 375 : 92-100

DOI: 10.1016/j.epsl.2013.05.014

Journal article

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Simplified detection of food-borne pathogens: An in situ high affinity capture and staining concept

T. Junillon, A. Vimont, D. Mosticone, B. Mallen, F. Baril, C. Rozand...

Journal of Microbiological Methods . 91 : 501--505

DOI: 10.1016/j.mimet.2012.09.015

Journal article

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Species-driven interpretation guidelines in case of a single-sampling strategy for blood culture

D. Leyssene, S. Gardes, P. Vilquin, Jp. Flandrois, Gérard Carret, B. Lamy

European Journal of Clinical Microbiology and Infectious Diseases . 30 : 1537-1541

DOI: 10.1007/s10096-011-1257-3

Journal article

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A pharmacologically based multiscale mathematical model of angiogenesis and its use in investigating the efficacy of a new cancer treatment strategy.

Frédérique Billy, Benjamin Ribba, Olivier Saut, Hélène Morre-Trouilhet, Thierry Colin, Didier Bresch...

Journal of Theoretical Biology . 260 ( 4 ) : 545-62

DOI: 10.1016/j.jtbi.2009.06.026

Journal article

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A seven-gene multilocus genus-wide approach to the phylogeny of mycobacteria using supertrees

S. Mignard, Jean-Pierre Flandrois

International Journal of Systematic and Evolutionary Microbiology . 58(part 6) : 1432-1441

Journal article

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Identification of Mycobacterium using the EF-Tu encoding (tuf) gene and the tmRNA encoding (ssrA) gene

S. Mignard, J.-P. Flandrois

Journal of Medical Microbiology . 56 ( 8 ) : 1033-1041

DOI: 10.1099/jmm.0.47105-0

Journal article

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Mycobacterium bovis Infection

S. Mignard, Jean-Pierre Flandrois

Journal of Medical Microbiology . 56 : 1033-1041

Journal article

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16S rRNA sequencing in routine bacterial identification : A 30-month experiment

S. Mignard, Jean-Pierre Flandrois

Journal of Microbiological Methods . 67 : 574-581

Journal article

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Rapid identification of Enterobacteriaceae by sequencing DNA gyrase subunit B encoding gene

J. Delmas, F. Breysse, G. Devulder, Jean-Pierre Flandrois, M. Chomarat

Diagnostic Microbiology and Infectious Disease . 55 : 263-268

Journal article

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Use of PCR-Restriction Enzyme Pattern Analysis and Sequencing Database for hsp65 Gene-Based Identification of Nocardia Species

V. Rodriguez-Nava, A. Couble, G. Devulder, Jean-Pierre Flandrois, P. Boiron, F. Laurent

Journal of Clinical Microbiology . 44 ( 2 ) : 536-546

DOI: 10.1128/JCM.44.2.536-546.2006

Journal article

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[From prevalence to predictive values: considerations on the antimicrobial susceptibility testing dealing with change of susceptibility rates].

Jean-Pierre Flandrois, B Lamy, G. Carret, M Delignette-Muller

Annales de Biologie Clinique . 63 ( 5 ) : 493-502

Journal article

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A multigene approach to phylogenetic analysis using the genus Mycobacterium as a model

G. Devulder, M. Perouse de Montclos, Jean-Pierre Flandrois

International Journal of Systematic and Evolutionary Microbiology . 55 : 293-302

Journal article

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De la prévalence aux valeurs prédictives: L`antibiogramme face à l`évolution de la résistance aux antibiotiques

B. Lamy, G. Carret, Jean-Pierre Flandrois, Marie Laure Delignette-Muller

Annales de Biologie Clinique . 63 : 493-502

Journal article

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How does susceptibility prevalence impact on the performance of disk diffusion susceptibility testing?

B. Lamy, G. Carret, Jean-Pierre Flandrois, Marie Laure Delignette-Muller

Diagnostic Microbiology and Infectious Disease . 49 : 131-139

Journal article

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Quelques problèmes statistiques rencontrés dans l`estimation de la température minimale de croissance de Listeria monocytogenes

S. Charles-Bajard, Jean-Pierre Flandrois, R. Tomassone

Revue de Statistique Appliquée . LI : 59-71

Journal article

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